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uniprot-database

Retrieve protein data from UniProt via REST endpoints for search, sequences, and ID mapping.

48|6|Updated Mar 9, 2026
Search Tags:#bioinformatics#rest-api#protein#uniprot#data-retrieval#id-mapping#fasta
One-click install
npx skills add https://github.com/qinyan-ai/qinyan-academic-skills --skill uniprot-database-qinyan-ai
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: uniprot-database
Source: https://github.com/qinyan-ai/qinyan-academic-skills/tree/main/skills/08-%E8%9B%8B%E7%99%BD%E8%B4%A8%E5%B7%A5%E7%A8%8B%E4%B8%8E%E7%BB%93%E6%9E%84%E7%94%9F%E7%89%A9%E5%AD%A6/uniprot-database
Command: npx skills add https://github.com/qinyan-ai/qinyan-academic-skills --skill uniprot-database-qinyan-ai

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires requests, and includes scripts (resource) and references (resource) components.

What problem does it solve?

UniProt provides exhaustive protein information but programmatic access requires manual API exploration. This Skill offers a ready-to-use REST-based workflow to search proteins, retrieve sequences, and map IDs for automated analysis.

Core Features & Use Cases

  • Unified REST API access for protein search, sequence retrieval, and ID mapping.
  • Python-based client with helper functions for search, retrieval, mapping, and streaming, plus practical examples.
  • Use cases include retrieving FASTA sequences, comparing Swiss-Prot vs. TrEMBL entries, and batch-processing multiple IDs.

Quick Start

Query a protein by accession (e.g., P01308) to retrieve its FASTA sequence via the REST API.

Frequently Asked Questions about uniprot-database

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I retrieve protein FASTA sequences from UniProt using a REST API?▼

You can retrieve protein FASTA sequences by querying the UniProt REST API endpoints with a specific protein accession like P01308. This skill provides a Python client with helper functions to fetch sequences directly for automated workflows.

What is the difference between Swiss-Prot and TrEMBL entries in UniProt?▼

Swiss-Prot contains manually reviewed and annotated protein entries, whereas TrEMBL holds computationally analyzed records. This skill allows you to search and access both types of annotations programmatically via the REST API.

How do I map protein IDs between different biological databases?▼

ID mapping translates identifiers from one database to another using the UniProt REST API. This skill supports batch processing of multiple IDs, allowing you to map accessions across different biological databases programmatically.

Can I batch process multiple protein accessions and stream large results from UniProt?▼

Yes, you can batch process multiple protein accessions and stream large result sets. The skill's Python client supports field customization and streaming to handle extensive protein data retrieval efficiently.

Do I need the requests library to programmatically access UniProt data?▼

Yes, the requests library is required as it serves as the underlying dependency for making REST API calls. The skill utilizes it within the Python client to execute searches, retrieve sequences, and perform ID mapping.

What is the best way to search for proteins by name or organism in UniProt?▼

The best way to search by name or organism is using the UniProt REST API search endpoints. This skill provides ready-to-use Python helper functions to query proteins based on specific biological criteria and retrieve matching data.

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